A few years ago, I was at a dinner party having a conversation with a couple, both cops, that really changed my views about religious influences in parenting.
The conversation had turned to parenting (not religious parenting, just parenting in general), and the husband started talking about lessons he'd taken away from his time as a cop (about 20 years at that point, IIRC). He said that he saw a common thread in almost every case he had to deal with where a teenager was victimized: the teen realized they were in a bad situation that was getting worse, but didn't think that they could call their parents for help and instead tried to get out of it themselves.
He told the people there that the best advice he could give to parents was to make sure that their children are never afraid to come to them with anything... that they should know that whatever happens, they'll be supported and protected.
Later on, I got to thinking about what sorts of things would make a child afraid to go to their parents when they need help, and I realized that most of them are much more likely to be issues in religious families than non-religious: homosexuality, alcohol consumption, premarital sex, etc.
While the degree to which a parent will try to impose religious ideas on their children does vary from religion to religion (and from parent to parent), I think that in general, it's fairly safe to say that the more a parent tries to impose beliefs and non-negotiable standards of behaviour on their child, the more this encourages a lack of willingness on the part of the child to share their life with the parent. And - for the reasons I just touched on - I think that the less open a child is with their parents, the greater risk of harm to the child.
And not only is there the risk of physical harm, it can be very distressing to a child to think that their "true" self wouldn't be accepted by their parents. I can't remember how many times I've heard stories from closeted atheist teens in religious homes in real anguish over the issue.
... and this occurs in very mainstream religious families. Even run-of-the-mill religious obligations like making the kids pray every day and go to church every Sunday can become downright oppressive if the child doesn't believe in the religion being forced on them.